BN1957 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 2.1535e-06 1.2750e-04
Layer 3 5.2820e-06 2.9173e-05
Layer 4 3.3202e-05 3.6305e-04
Layer 5 1.8760e-03 5.1378e-03
Layer 1 9.6853e-01 3.0244e-01
Layer 6 9.9996e-01 2.8107e-01
WM 1.0000e+00 1.5203e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
NSG2 Expression Distribution
Gene Specificity Score (GSS)
NSG2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
NSG2 Layer 3 3.7969 0.8648
NRXN1 Layer 3 4.1094 0.8647
ATP2B2 Layer 3 4.4590 0.8642
SLC12A5 Layer 3 3.6211 0.8627
FXYD7 Layer 3 3.7637 0.8617
ZBTB18 Layer 3 3.7070 0.8591
MEG3 Layer 2 4.1016 0.8579
SERPINI1 Layer 3 3.3789 0.8566
C11orf87 Layer 3 3.1494 0.8565
MEF2C Layer 3 4.0703 0.8556
NAP1L2 Layer 3 3.2500 0.8553
GABRA1 Layer 3 3.9160 0.8550
RUNDC3A Layer 4 3.7520 0.8547
PIN1 Layer 3 3.5176 0.8546
DMTN Layer 3 3.7480 0.8534
CDIP1 Layer 3 3.3574 0.8533
PPP3R1 Layer 3 3.2822 0.8522
ATP1A3 Layer 3 3.9980 0.8515
AGAP3 Layer 3 3.4346 0.8514
GRIN1 Layer 3 3.9980 0.8512
SYN1 Layer 2 3.7559 0.8501
PLD3 Layer 3 3.3789 0.8496
RASD1 Layer 3 3.6523 0.8494
CA11 Layer 4 3.6992 0.8482
SNCB Layer 3 3.9160 0.8476
ADCY1 Layer 3 3.4453 0.8474
NPTN Layer 3 3.6328 0.8473
ARF1 Layer 3 3.2422 0.8472
MRTFB Layer 2 3.3945 0.8471
PSD3 Layer 2 4.2891 0.8471
PIP4K2B Layer 3 3.3975 0.8470
DGKZ Layer 4 3.6719 0.8466
INPP5F Layer 3 3.4453 0.8463
PRRT1 Layer 3 3.3252 0.8461
HOPX Layer 2 4.6250 0.8460
VSTM2A Layer 3 4.1758 0.8458
STX1B Layer 4 3.3438 0.8457
FAIM2 Layer 3 3.3438 0.8455
SYT13 Layer 3 3.4609 0.8452
SV2A Layer 3 3.5547 0.8448
SIRPA Layer 3 3.5703 0.8442
TMEM59L Layer 3 3.6523 0.8436
NCS1 Layer 3 3.3223 0.8428
TSPYL4 Layer 2 3.3145 0.8428
PPP2R1A Layer 4 3.3359 0.8428
TERF2IP Layer 2 3.2285 0.8427
INA Layer 3 4.0156 0.8427
NCDN Layer 2 3.7969 0.8423
AUXG01000058.1 Layer 3 3.6914 0.8421
HSPH1 Layer 3 3.7402 0.8415

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1957
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1957_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1957/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1957/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1957/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1957/report/PD/BN1957_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1957/report/PD/BN1957_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:03:48
  • Number of Processes: 10
  • Spending Time: 0h 4m